[gmx-users] potential energy

[Justin Lemkul]

On 1/10/15 3:52 PM, mah maz wrote:
> Dear all,
> I wanted to know if the potential energy gained by "g_energy -f ener.edr
> -o" the total potential energy of the system or partial ones like vdw
> energy. If it is the total energy, to my knowledge it should be negative,

It's the full potential energy.  Various components are also printed out to the 
various energy terms printed by g_energy.

> and its summation with the kinetic energy should be negative showing the
> stability of the system. In my simulation, potential energy is positive and
> the total energy is a big positive number, but no explosion happened. What
> is the problem?

That depends entirely upon what your system is.  A negative potential is 
generally expected for most condensed-phase systems, in which attractive 
nonbonded interactions dominate over repulsive terms.  But the energy of a given 
system is entirely dependent upon what the system is.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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